Sequences associated with tdp-43 proteinopathies and methods of using the same

ABSTRACT

The present invention provides nucleic acids and peptides, and methods of using the nucleic acids and peptides to identify subjects at risk for a TDP-43 proteinopathy. The invention also provides for an array comprising the nucleic acids and peptides of the invention.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the priority of U.S. Ser. No. 12/865,659, filedJan. 30, 2009, which claims priority to PCT/US09/32627, filed Nov. 22,2010, which claims priority to U.S. provisional application No.61,025,377, filed Feb. 1, 2008, which is hereby incorporated byreference in its entirety.

GOVERNMENTAL RIGHTS

This invention was made with government support under P50-AG05681awarded by the National Institutes of Health. The government has certainrights in the invention.

FIELD OF THE INVENTION

The present invention provides nucleic acid and amino acid sequencesthat may be utilized to identify subjects at risk for a TDP-43proteinopathy.

BACKGROUND OF THE INVENTION

TAR DNA-binding protein 43 (TDP-43) is a pathological protein ofsporadic and familial frontotemporal lobar degeneration (FTLD) withubiquitin-positive, tau-negative inclusions (FTLD-U) with or withoutmotor neuron disease (MND). MND is a neurodegenerative disorderinvolving the loss of upper and/or lower motor neurons and ischaracterized clinically by progressive weakness and death within a fewyears of onset; the most common clinical MND phenotype is amyotrophiclateral sclerosis (ALS). Recently, TAR DNA-binding protein 43 (TDP-43)was identified as a pathological protein of the motor neuron inclusionsfound in sporadic MND, but not in familial MND with Cu/Zn superoxidedismutase-1 (SOD1) mutation.¹⁻⁴ TDP-43 thus defines a class ofneurodegenerative diseases referred to as TDP-43 proteinopathies. Thereis a need in the art for understanding the link between TDP-43 and thesediseases, such that diagnostic and therapeutic treatments may bedeveloped.

SUMMARY OF THE INVENTION

One aspect of the invention encompasses an isolated nucleic acidcomprising at least ten contiguous nucleotides, including nucleotide1077, of SEQ ID NO: 1.

Another aspect of the invention encompasses an isolated peptidecomprising at least ten contiguous amino acids, including amino acid315, of SEQ ID NO: 2.

Yet another aspect of the invention encompasses a method for identifyinga subject at risk for a TDP-43 proteinopathy. The method comprisesdetermining the identity of the nucleotide at position 1077 of anucleotide sequence comprising the nucleic acid sequence of SEQ ID NO: 1in a sample from a subject. The presence of a G instead of an A atnucleotide 1077 indicates a risk for a TDP-43 proteinopathy.

An additional aspect of the invention encompasses a method foridentifying a subject at risk for a TDP-43 proteinopathy. The methodcomprises determining the identity of the amino acid at position 315 ofan amino acid sequence comprising the amino acid sequence of SEQ ID NO:2 in a sample from a subject. The presence of a threonine instead of analanine at amino acid 315 indicates a risk for a TDP-43 proteinopathy.

A further aspect of the invention encompasses an array that comprises anaddress comprising an epitope binding agent. In one iteration, theepitope binding agent can specifically bind to SEQ ID NO: 1 or a portionthereof containing nucleotide 1077. Alternatively, the epitope bindingagent can specifically bind to SEQ ID NO: 2 or a portion thereofcontaining amino acid 315.

Other aspects and iterations of the invention are described morethoroughly below.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 depicts illustrations showing that the missense mutation A315Twithin a highly conserved region of exon 6 of TDP-43 segregates with allaffected members of an autosomal dominant MND family. (a) TDP-43 genomicstructure, position of missense mutation, and location of amino acidchange adjacent to glycine-rich domain. (b) Chromatogram of exon 6displays a base pair change (c.1077 G>A) compared to family control. (c)Pedigree of family displays segregation of the mutation with disease(⋄=unaffected, ♦=affected with mutation, diagonal line=deceased). Rsalrestriction digest was used to screen family members and 1,505 controls.Direct sequencing was also performed on all family members in this studyto verify the mutation.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides a nucleic acid sequence variant of TDP-43(SEQ ID NO: 1 in Table 1) that is associated with TDP-43proteinopathies. In particular, nucleic acid 1077 of SEQ ID NO: 1 is anA, as opposed to a G. Additionally, the invention provides an amino acidsequence variant (SEQ ID NO: 2 in Table 1) of TDP-43 that is associatedwith TDP-43 proteinopathies. In particular, amino acid 315 of SEQ ID NO:2 is a threonine, as opposed to an alanine. The invention alsoencompasses methods of diagnosing or detecting a TDP-43 proteinopathy ina subject and an array. The sequences for SEQ ID Nos. 1, 2, 3, and 4 areshown in Table 1 below.

TABLE 1 SEQ IDggtgggcggggggaggaggcggccctagcgccattttgtgggagcgaagcggtggctgggctgcgcttgggtccgtcgctgcttNO: 1cggtgtccctgtcgggcttcccagcagcggcctagcgggaaaagtaaaagatgtctgaatatattcgggtaaccgaagatgagaacgatgagcccattgaaataccatcggaagacgatgggacggtgctgctctccacggttacagcccagtttccaggggcgtgtgggcttcgctacaggaatccagtgtctcagtgtatgagaggtgtccggctggtagaaggaattctgcatgccccagatgctggctggggaaatctggtgtatgttgtcaactatccaaaagataacaaaagaaaaatggatgagacagatgcttcatcagcagtgaaagtgaaaagagcagtccagaaaacatccgatttaatagtgttgggtctcccatggaaaacaaccgaacaggacctgaaagagtattttagtacctttggagaagttcttatggtgcaggtcaagaaagatcttaagactggtcattcaaaggggtttggctttgttcgttttacggaatatgaaacacaagtgaaagtaatgtcacagcgacatatgatagatggacgatggtgtgactgcaaacttcctaattctaagcaaagccaagatgagcctttgagaagcagaaaagtgtttgtggggcgctgtacagaggacatgactgaggatgagctgcgggagttcttctctcagtacggggatgtgatggatgtcttcatccccaagccattcagggcctttgcctttgttacatttgcagatgatcagattgcgcagtctctttgtggagaggacttgatcattaaaggaatcagcgttcatatatccaatgccgaacctaagcacaatagcaatagacagttagaaagaagtggaagatttggtggtaatccaggtggctttgggaatcagggtggatttggtaatagcagagggggtggagctggtttgggaaacaatcaaggtagtaatatgggtggtgggatgaactttggtacgttcagcattaatccagccatgatggctgccgcccaggcagcactacagagcagttggggtatgatgggcatgttagccagccagcagaaccagtcaggcccatcgggtaataaccaaaaccaaggcaacatgcagagggagccaaaccaggccttcggttctggaaataactcttatagtggctctaattctggtgcagcaattggttggggatcagcatccaatgcagggtcgggcagtggttttaatggaggctttggctcaagcatggattctaagtcttctggctggggaatgtagacagtggggttgtggttggttggtatagaatggtgggaattcaaatttttctaaactcatggtaagtatattgtaaaatacatatgtactaagaattttcaaaattggtttgttcagtgtggagtatattcagcagtatttttgacatttttctttagaaaaaggaagagctaaaggaattttataagttttgttacatgaaaggttgaaatattgagtggttgaaagtgaactgctgtttgcctgattggtaaaccaacacactacaattgatatcaaaaggtttctcctgtaatattttatccctggacttgtcaagtgaattctttgcatgttcaaaacggaaaccattgattagaactacattctttaccccttgttttaatttgaaccccaccatatggatttttttccttaagaaaatctccttttaggagatcatggtgtcacagtgtttggttcttttgttttgttttttaacacttgtctcccctcatacacaaaagtacaatatgaagccttcatttaatctctgcagttcatctcatttcaaatgtttatggaagaagcacttcattgaaagtagtgctgtaaatattctgccataggaatactgtctacatgctttctcattcaagaattcgtcatcacgcatcacaggccgcgtctttgacggtgggtgtcccatttttatccgctactctttatttcatggagtcgtatcaacgctatgaacgcaaggctgtgatatggaaccagaaggctgtctgaacttttgaaaccttgtgtgggattgatggtggtgccgaggcatgaaaggctagtatgagcgagaaaaggagagagcgcgtgcagagacttggtggtgcataatggatattttttaacttggcgagatgtgtctctcaatcctgtggctttggtgagagagtgtgcagagagcaatgatagcaaataatgtacgaatgttttttgcattcaaaggacatccacatctgttggaagacttttaagtgagtttttgttcttagataacccacattagatgaatgtgttaagtgaaatgatacttgtactccccctacccctttgtcaactgctgtgaatgctgtatggtgtgtgttctcttctgttactgatatgtaagtgtggcaatgtgaactgaagctgatgggctgagaacatggactgagcttgtggtgtgctttgcaggaggacttgaagcagagttcaccagtgagctcaggtgtctcaaagaagggtggaagttctaatgtctgttagctacccataagaatgctgtttgctgcagttctgtgtcctgtgcttggatgctttttataagagttgtcattgttggaaattcttaaataaaactgatttaaataatatgtgtctttgttttgcagccctgaatgcaaagaattcatagcagttaattccccttttttgacccttttgagatggaactttcataaagtttcttggcagtagtttattttgcttcaaataaacttatttgaaaagttgtctcaagtcaaatggattcatcacctgtcatgcattgacacctgatacccagacttaattggtatttgttcttgcattggccaaagtgaaaatttttttttttcttttgaaatctagttttgaataagtctgggtgaccgcacctaaaatggtaagcagtaccctccggctttttcttagtgcctctgtgcatttgggtgatgttctatttacatggcctgtgtaaatctccattgggaagtcatgccttctaaaaagattcttatttgggggagtgggcaaaatgttgattattttctaatgctttgtagcaaagcatatcaattgaaaagggaatatcagcaccttcctagtttgggatttgaaaagtggaattaattgcagtagggataaagtagaagaaaccacaaattatcttgtgcctgaaatccattaagaggcctgatagctttaagaattagggtgggttgtctgtctggaagtgttaagtggaatgggctttgtcctccaggaggtgggggaatgtggtaacattgaatacagttgaataaaatcgcttacaaaactcacactctcacaatgcattgttaagtatgtaaaagcaataacattgattctctgttgtacttttttgtaactaattctgtgagagttgagctcattttctagttggaagaatgtgatatttgttgtgttggtagtttacctaatgcccttacctaattagattatgataaataggtttgtcattttgcaagttacataaacatttatcaatgaagtcatcctttagacttgtaatcgccacattgtttcattattcagtttcctctgtaaagggatcttgagttgttttaattttttttttctgcatctgaatctgcatgatttccaaaccctgtaccatctgaattttgcattttagcacttgcactattactcagcagcagtaacatggtaacacttaaaatggtactcggggacctccaaagactaaactgacaagccttcaaggagcccaggggtaagttaacttgtcaacggcatggtttaatcccttctttacacttgtgtaaatttcagttactggtcatagaaggctttcaatgttgagtggccttttattaacatgtttatggtactgcatagatacgggtatttattttaccctaagaagattttgaagtttaaaagtacttaaactatttggcaaagatttgtttttaaaaatctatttggtcaatctaaatgcattcattctaaaaaattttttgaaccagataaataaaatttttttttgacaccacaaaaaaaaaaaaaaaaaaaa SEQ IDMSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILH NO: 2APDAGWGNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDEPLRSRKVFVGRCTEDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNSNRQLERSGRFGGNPGGFGNQGGFGNSRGGGAGLGNNQGSNMGGGMNFGTFSINPAMMAAAQAALQSSWGMMGMLASQQNQSGPSGNNQNQGNMQREPNQAFGSGNNSYSGSNSGAAIGWGSASNAGSGSGFNGGFGSSMDSKSSGWGM SEQ IDggtgggcggggggaggaggcggccctagcgccattttgtgggagcgaagcggtggctgggctgcgcttgggtccgtcgctgcttNO: 3cggtgtccctgtcgggcttcccagcagcggcctagcgggaaaagtaaaagatgtctgaatatattcgggtaaccgaagatgagaacgatgagcccattgaaataccatcggaagacgatgggacggtgctgctctccacggttacagcccagtttccaggggcgtgtgggcttcgctacaggaatccagtgtctcagtgtatgagaggtgtccggctggtagaaggaattctgcatgccccagatgctggctggggaaatctggtgtatgttgtcaactatccaaaagataacaaaagaaaaatggatgagacagatgcttcatcagcagtgaaagtgaaaagagcagtccagaaaacatccgatttaatagtgttgggtctcccatggaaaacaaccgaacaggacctgaaagagtattttagtacctttggagaagttcttatggtgcaggtcaagaaagatcttaagactggtcattcaaaggggtttggctttgttcgttttacggaatatgaaacacaagtgaaagtaatgtcacagcgacatatgatagatggacgatggtgtgactgcaaacttcctaattctaagcaaagccaagatgagcctttgagaagcagaaaagtgtttgtggggcgctgtacagaggacatgactgaggatgagctgcgggagttcttctctcagtacggggatgtgatggatgtcttcatccccaagccattcagggcctttgcctttgttacatttgcagatgatcagattgcgcagtctctttgtggagaggacttgatcattaaaggaatcagcgttcatatatccaatgccgaacctaagcacaatagcaatagacagttagaaagaagtggaagatttggtggtaatccaggtggctttgggaatcagggtggatttggtaatagcagagggggtggagctggtttgggaaacaatcaaggtagtaatatgggtggtgggatgaactttggtgcgttcagcattaatccagccatgatggctgccgcccaggcagcactacagagcagttggggtatgatgggcatgttagccagccagcagaaccagtcaggcccatcgggtaataaccaaaaccaaggcaacatgcagagggagccaaaccaggccttcggttctggaaataactcttatagtggctctaattctggtgcagcaattggttggggatcagcatccaatgcagggtcgggcagtggttttaatggaggctttggctcaagcatggattctaagtcttctggctggggaatgtagacagtggggttgtggttggttggtatagaatggtgggaattcaaatttttctaaactcatggtaagtatattgtaaaatacatatgtactaagaattttcaaaattggtttgttcagtgtggagtatattcagcagtatttttgacatttttctttagaaaaaggaagagctaaaggaattttataagttttgttacatgaaaggttgaaatattgagtggttgaaagtgaactgctgtttgcctgattggtaaaccaacacactacaattgatatcaaaaggtttctcctgtaatattttatccctggacttgtcaagtgaattctttgcatgttcaaaacggaaaccattgattagaactacattctttaccccttgttttaatttgaaccccaccatatggatttttttccttaagaaaatctccttttaggagatcatggtgtcacagtgtttggttcttttgttttgttttttaacacttgtctcccctcatacacaaaagtacaatatgaagccttcatttaatctctgcagttcatctcatttcaaatgtttatggaagaagcacttcattgaaagtagtgctgtaaatattctgccataggaatactgtctacatgctttctcattcaagaattcgtcatcacgcatcacaggccgcgtctttgacggtgggtgtcccatttttatccgctactctttatttcatggagtcgtatcaacgctatgaacgcaaggctgtgatatggaaccagaaggctgtctgaacttttgaaaccttgtgtgggattgatggtggtgccgaggcatgaaaggctagtatgagcgagaaaaggagagagcgcgtgcagagacttggtggtgcataatggatattttttaacttggcgagatgtgtctctcaatcctgtggctttggtgagagagtgtgcagagagcaatgatagcaaataatgtacgaatgttttttgcattcaaaggacatccacatctgttggaagacttttaagtgagtttttgttcttagataacccacattagatgaatgtgttaagtgaaatgatacttgtactccccctacccctttgtcaactgctgtgaatgctgtatggtgtgtgttctcttctgttactgatattgtaagtgtggcaatgtgaactgaagctgagggctgagaacatggactgagcttgtggtgtgctttgcaggaggacttgaagcaagagttcaccagtgagctcaggtgtctcaaagagggtggaagttctaatgtctgttagctacccataagaatgctgtttgctgcagttctgtgtcctgtgcttggatgctttttataagagttgtcattgttggaaattcttaaataaaactgatttaaataatatgtgtctttgttttgcagccctgaatgcaaagaattcatagcagttaattccccttttttgacccttttgagatggaactttcataaagtttcttggcagtagtttattttgcttcaaataaacttatttgaaaagttgtctcaagtcaaatggattcatcacctgtcatgcattgacacctgatacccagacttaattggtatttgttcttgcattggccaaagtgaaaatttttttttttcttttgaaatctagttttgaataagtctgggtgaccgcacctaaaatggtaagcagtaccctccggctttttcttagtgcctctgtgcatttgggtgatgttctatttacatggcctgtgtaaatctccattgggaagtcatgccttctaaaaagattcttatttgggggagtgggcaaaatgttgattattttctaatgctttgtagcaaagcatatcaattgaaaagggaatatcagcaccttcctagtttgggatttgaaaagtggaattaattgcagtagggataaagtagaagaaaccacaaattatcttgtgcctgaaatccattaagaggcctgatagctttaagaattagggtgggttgtctgtctggaagtgttaagtggaatgggctttgtcctccaggaggtgggggaatgtggtaacattgaatacagttgaataaaatcgcttacaaaactcacactctcacaatgcattgttaagtatgtaaaagcaataacattgattctctgttgtacttttttgtaactaattctgtgagagttgagctcattttctagttggaagaatgtgatatttgttgtgttggtagttatacctaatgcccttacctaattagattatgataataggtttgtcattttgcaagttacataaacatttatcaatgaagtcatcctttagacttgtaatcgccacattgtttcattattcagtttcctctgtaaagggatcttgagttgttttaattttttttttctgcatctgaatctgcatgatttccaaaccctgtaccatctgaattttgcattttagcacttgcactattactcagcagcagtaacatggtaacacttaaaatggtactcggggacctccaaagactaaactgacaagccttcaaggagcccaggggtaagttaacttgtcaacggcatggtttaatcccttctttacacttgtgtaaatttcagttactggtcatagaaggctttcaatgttgagtggccttttattaacatgtttatggtactgcatagatacgggtatttattttaccctaagaagattttgaagtttaaaagtacttaaactatttggcaaagatttgtttttaaaaatctatttggtcaatctaaatgcattcattctaaaaaattttttgaaccagataaataaaatttttttttgacaccacaaaaaaaaaaaaaaaaaaaa SEQ IDMSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILH NO: 4APDAGWGNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDEPLRSRKVFVGRCTEDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNSNRQLERSGRFGGNPGGFGNQGGFGNSRGGGAGLGNNQGSNMGGGMNFGAFSINPAMMAAAQAALQSSWGMMGMLASQQNQSGPSGNNQNQGNMQREPNQAFGSGNNSYSGSNSGAAIGWGSASNAGSGSGFNGGFGSSMDSKSSGWGM

I. Nucleic Acid

One aspect of the present invention encompasses an isolated nucleicacid. Generally speaking, the sequence of the nucleic acid comprisesnucleotide position 1077 of SEQ ID NO: 1. In particular, the sequence ofthe nucleic acid comprises an A at position 1077 of SEQ ID NO: 1, asopposed to the wild-type sequence that has a G at position 1077 (SEQ IDNO: 3, Table 1). In one embodiment, the nucleic acid comprises at leastfive contiguous nucleotides, including nucleotide 1077, of SEQ ID NO: 1.In another embodiment, the nucleic acid comprises at least 10, at least15, at least 20, at least 25, at least 30, at least 35, at least 40, atleast 45, at least 50, at least 55, at least 60, at least 65, at least70, at least 75, at least 80, at least 85, at least 90, at least 95, orat least 100 contiguous nucleotides, including nucleotide 1077, of SEQID NO: 1. In yet another embodiment, the nucleic acid comprises at least200, at least 300, at least 400, at least 500, at least 600, at least700, at least 800, at least 900, or at least 1000 contiguousnucleotides, including nucleotide 1077, of SEQ ID NO: 1. In a furtherembodiment, the nucleic acid comprises at least 1000, at least 2000, atleast 3000, at least 4000, or more than 4000 contiguous nucleotides,including nucleotide 1077, of SEQ ID NO: 1.

In an alternative embodiment, the nucleic acid comprises exon 6 ofTDP-43, wherein nucleic acid 1077 is an A instead of a G. In anotheralternative embodiment, the nucleic acid comprises the cDNA of TDP-43,wherein nucleic acid 1077 is an A instead of a G. In certainembodiments, the nucleic acid consists of the nucleic acid sequence ofSEQ ID NO: 1.

The present invention also encompasses nucleic acids that arecomplementary to the isolated nucleic acid sequences described above.For instance, in some embodiments, a nucleic acid of the inventionhybridizes to a nucleic acid comprising nucleotide position 1077 of SEQID NO: 1. In other embodiments, the nucleic acid hybridizes to a nucleicacid comprising nucleotide 1077 of SEQ ID NO: 1 but not to a nucleicacid comprising nucleotide 1077 of SEQ ID NO: 3. In one embodiment, thenucleic acid hybridizes to a nucleic acid comprising exon 6 of TDP-43,wherein nucleic acid 1077 is an A instead of a G.

Hybridization of nucleic acids is typically performed under stringentconditions. Nucleic acid duplex or hybrid stability is expressed as themelting temperature or Tm, which is the temperature at which a probedissociates from a target DNA. This melting temperature is used todefine the required stringency conditions. To maximize the rate ofannealing of the probe with its target, hybridizations are generallycarried out at a temperature that is about 20 to 25° C. below the Tm.For instance, stringent conditions may typically involve hybridizing atabout 68° C. in 5x SSC/5x Denhardt's solution/1.0% SDS, and washing in0.2x SSC/0.1% SDS at about 68° C. Moderately stringent conditionsinclude washing in 3x SSC at 42° C. The parameters of salt concentrationand temperature can be varied to achieve the optimal level of identitybetween the nucleic acid and the target sequence, for instance, asequence comprising nucleotide 1077 of SEQ ID NO: 1. One skilled in theart will appreciate which parameters to manipulate to optimizehybridization. Additional guidance regarding such conditions is readilyavailable in the art, for example, by Sambrook et al., 1989, MolecularCloning, A Laboratory Manual, Cold Spring Harbor Press, N.Y.; andAusubel et al., (eds.), 1995, Current Protocols in Molecular Biology,(John Wiley & Sons, N.Y.) at Unit 2.10.

The isolated nucleic acids of the invention may be labeled. Non-limitingexamples of suitable labels may include fluorescent labels,chemiluminescent labels, radioactive labels, colorimetric labels, andresonance labels. Methods of labeling nucleic acids are well known inthe art.

The various nucleic acids mentioned above may be obtained using avariety of different techniques known in the art. The nucleic acids maybe isolated using standard techniques, may be synthesized using standardtechniques, or may be purchased or obtained from a depository. Once thenucleic acid is obtained, it may be amplified and/or sequenced for usein a variety of applications, e.g. the methods described below.

The invention also encompasses production of nucleic acids comprisingnucleotide 1077 of SEQ ID NO: 1, or derivatives or fragments thereof,that may be made by any method known in the art, including by syntheticchemistry. After production, the synthetic sequence may be inserted intoany of the many available expression vectors and cell systems usingreagents well known in the art.

II. Peptide

Another aspect of the present invention encompasses an isolated peptide.Generally speaking, the amino acid sequence of the peptide comprises theamino acid at position 315 of SEQ ID NO: 2. In particular, the sequenceof the peptide comprises threonine at position 315 of SEQ ID NO: 2, asopposed to the wild-type sequence that has an alanine at position 315(SEQ ID NO: 4 in Table 1). In one embodiment, the peptide comprises atleast five contiguous amino acids, including amino acid 315, of SEQ IDNO: 2. In another embodiment, the peptide comprises at least 10, atleast 15, at least 20, at least 25, at least 30, at least 35, at least40, at least 45, at least 50, at least 55, at least 60, at least 65, atleast 70, at least 75, at least 80, at least 90 or at least 100contiguous amino acids, including amino acid 315, of SEQ ID NO: 2. Inyet another embodiment, the peptide comprises at least 200, at least300, at least 400 or at least 500 contiguous amino acids, includingamino acid 315, of SEQ ID NO: 2.

In an alternative embodiment, the peptide comprises the translated aminoacid sequence of exon 6 of TDP-43, wherein amino acid 315 is athreonine. In yet another alternative, the peptide consists of the aminoacid sequence of TDP-43, wherein amino acid 315 is a threonine.

The isolated peptide of the invention may be labeled. Non-limitingexamples of suitable labels include fluorescent labels, chemiluminescentlabels, radioactive labels, colorimetric labels, and resonance labels.Methods of labeling peptides are well known in the art.

The various peptides mentioned above may be obtained using a variety ofdifferent techniques known in the art. The peptides may be isolatedusing standard techniques, may be synthesized using standard techniques,or may be purchased or obtained from a depository.

The invention also encompasses production of peptides comprising aminoacid 315 of SEQ ID NO: 2, or derivatives or fragments thereof, that maybe made by any method known in the art, including by syntheticchemistry.

III. Methods

Yet another aspect of the invention encompasses methods for determiningrisk and diagnosis of a TDP-43 proteinopathy. As used herein, a TDP-43proteinopathy is a disorder or a disease characterized in part by amutation or malfunction of the TDP-43 protein. In an exemplaryembodiment, a TDP-43 proteinopathy is a disease or a disordercharacterized in part by the substitution of the guanine at nucleotide1077 of SEQ ID NO: 3 to an adenine resulting in the nucleic acidsequence variant of SEQ ID NO: 1, or the substitution of the alanine atamino acid 315 of SEQ ID NO: 4 to a threonine resulting in the aminoacid sequence variant of SEQ ID NO: 2. Non-limiting examples of a TDP-43proteinopathy may include sporadic frontotemporal lobar degeneration(FTLD), also called frontotemporal dementia, familial FTLD, sporadicMND, familial MND, sporadic ALS, and familial ALS, and combinations ofthese two motor and cognitive phenotypes, including FTLD-MND.

In one embodiment, the invention provides a method for determiningwhether a subject is at risk for a TDP-43 proteinopathy. For instance,in some embodiments, the invention provides a method for determiningwhether a subject is at risk for ALS. Generally speaking, the methodcomprises determining whether the subject has an adenine at nucleotide1077 of TDP-43 instead of a guanine. If an adenine is present, thesubject may be at risk for developing a TDP-43 proteinopathy.Alternatively, the method may comprise determining whether the subjecthas a threonine at amino acid 315 of TDP-43 instead of an alanine. If athreonine is present, the subject may be at risk for developing a TDP-43proteinopathy.

In another embodiment, the invention provides a method for diagnosing asubject with a TDP-43 proteinopathy. For instance, in some embodiments,the invention provides a method for diagnosing a subject with ALS.Typically, the method comprises determining whether the subject has anadenine at nucleotide 1077 of TDP-43 instead of a guanine. If an adenineis present, the subject may be diagnosed with a TDP-43 proteinopathy.Alternatively, the method may comprise determining whether the subjecthas a threonine at amino acid 315 of TDP-43 instead of an alanine. If athreonine is present, the subject may be diagnosed with a TDP-43proteinopathy.

Methods for determining whether a subject has an adenine at nucleotide1077 of TDP-43 instead of a guanine are known in the art. For instance,sequencing of a portion of TDP-43 encompassing nucleotide 1077 may beperformed as detailed in the examples. Alternatively, an array may beused as detailed below.

In certain embodiments, nucleic acid from a subject may be digested witha restriction enzyme that generates a unique fragment in a subject withan adenine at nucleotide 1077 of TDP-43 instead of a guanine. Forinstance, the restriction enzyme Rsa1 may be used. Rsa1 generates aunique fragment when incubated with a nucleic acid comprising exon 6 ofTDP-43 when nucleotide 1077 is an adenine. The fragment may be amplifiedfrom genomic DNA using the polymerase chain reaction method. Forinstance, see FIG. 1C.

Similarly, methods for determining whether a subject has a threonine atamino acid 315 of TDP-43 instead of an alanine are known in the art. Forinstance, an array may be used as detailed below. Alternatively anantibody that recognizes a threonine at position 315, but not analanine, may be used.

Methods of obtaining a nucleic acid and/or a peptide of the inventionfrom a subject are known in the art. For instance, biological samplescomprising a nucleic acid and/or a peptide of the invention may becollected from a subject. Non-limiting examples of suitable biologicalsamples may include blood samples, tissues samples, or bodily fluidsamples. Blood samples may include whole blood, serum, or plasma. Bodilyfluid samples may include urine, lymph, or saliva samples.

Suitable subjects express TDP-43. For instance, humans, non-humanprimates, rodents, livestock animals, and companion animals arenon-limiting examples of suitable subjects. Rodents may include mice,rats, and guinea pigs. Livestock animals may include cattle, swine, andchicken. Companion animals may include cats and dogs. In someembodiments, the subject is a frog. In each of the above embodiments,the subject may have a family history of a TDP-43 proteinopathy, of aMND, or of FTLD. Alternatively, the subject may have symptoms of aTDP-43 proteinopathy, of a MND, or of a FTLD. In some embodiments, thesubject may have no clinical symptoms of a TDP-43 proteinopathy, of aMND, or of a FTLD.

IV. Array

A further aspect of the invention is an array comprising at least oneaddress. In some embodiments, at least one address of the array hasdisposed thereon an epitope binding agent that can specifically bind toSEQ ID NO: 1, or a portion thereof, containing nucleotide 1077. In otherembodiments, at least one address of the array has disposed thereon anepitope binding agent that can specifically bind to SEQ ID NO: 2, or aportion thereof, containing amino acid 315.

Several substrates suitable for the construction of arrays are known inthe art, and one skilled in the art will appreciate that othersubstrates may become available as the art progresses. The substrate maybe a material that may be modified to contain discrete individual sitesappropriate for the attachment or association of an epitope bindingagent and is amenable to at least one detection method. Non-limitingexamples of substrate materials include glass, modified orfunctionalized glass, plastics (including acrylics, polystyrene andcopolymers of styrene and other materials, polypropylene, polyethylene,polybutylene, polyurethanes, TeflonJ, etc.), nylon or nitrocellulose,polysaccharides, nylon, resins, silica or silica-based materialsincluding silicon and modified silicon, carbon, metals, inorganicglasses and plastics. In an exemplary embodiment, the substrate mayallow optical detection without appreciably fluorescing.

A substrate may be planar, a substrate may be a well, i.e. a 364 wellplate, or alternatively, a substrate may be a bead. Additionally, thesubstrate may be the inner surface of a tube for flow-through sampleanalysis to minimize sample volume. Similarly, the substrate may beflexible, such as a flexible foam, including closed cell foams made ofparticular plastics.

An epitope binding agent may be attached to the substrate in a widevariety of ways, as will be appreciated by those in the art. The nucleicacid or epitope binding agent may either be synthesized first, withsubsequent attachment to the substrate, or may be directly synthesizedon the substrate. The substrate and the epitope binding agent may bederivatized with chemical functional groups for subsequent attachment ofthe two. For example, the substrate may be derivatized with a chemicalfunctional group including, but not limited to, amino groups, carboxylgroups, oxo groups or thiol groups. Using these functional groups, theepitope binding agent may be attached using functional groups on thenucleic acid or epitope binding agent either directly or indirectlyusing linkers.

The epitope binding agent may also be attached to the substratenon-covalently. For example, a biotinylated epitope binding agent may beprepared, which may bind to surfaces covalently coated withstreptavidin, resulting in attachment. Alternatively, an epitope bindingagent may be synthesized on the surface using techniques such asphotopolymerization and photolithography. Additional methods ofattaching epitope binding agents to arrays and methods of synthesizingbiomolecules on substrates are well known in the art, i.e. VLSIPStechnology from Affymetrix (e.g., see U.S. Pat. No. 6,566,495, andRockett and Dix, Xenobiotica 30(2): 155-177, both of which are herebyincorporated by reference in their entirety).

In one embodiment, the epitope binding agent attached to the substrateis located at a spatially defined address of the array. Arrays maycomprise from about 1 to about several hundred thousand addresses. Inone embodiment, the array may be comprised of less than 10,000addresses. In another alternative embodiment, the array may be comprisedof at least 10,000 addresses. In yet another alternative embodiment, thearray may be comprised of less than 5,000 addresses. In still anotheralternative embodiment, the array may be comprised of at least 5,000addresses. In a further embodiment, the array may be comprised of lessthan 500 addresses. In yet a further embodiment, the array may becomprised of at least 500 addresses.

An epitope binding agent may be represented more than once on a givenarray. In other words, more than one address of an array may becomprised of the same epitope binding agent. In some embodiments, two,three, or more than three addresses of the array may be comprised of thesame epitope binding agent. In certain embodiments, the array maycomprise control epitope binding agents and/or control addresses. Thecontrols may be internal controls, positive controls, negative controls,or background controls.

As used herein, “epitope binding agent” may refer to a nucleic acid, anoligonucleic acid, an amino acid, a peptide, a polypeptide, a protein, alipid, a metabolite, a small molecule or a fragment thereof thatrecognizes and is capable of binding to SEQ ID NO: 2 or a portionthereof containing amino acid 315, or to SEQ ID NO: 1 or a portionthereof containing nucleic acid 1077. Nucleic acids may include RNA,DNA, and naturally occurring or synthetically created derivatives.

In further embodiments, an epitope binding agent of the array mayrecognize mutations in one or more of the sequences selected from thegroup of sequences comprising the vesicle-associated membraneprotein-associated protein B (VAPB), dynactin (DCTN1), alsin (ALS2),immunoglobulin μ binding protein 2 (IGHMBP2), or glycyl-tRNA synthetase(GARS) genes that are associated with MND.

The arrays may be utilized in several suitable applications. Forexample, the arrays may be used in methods for detecting associationbetween an epitope binding agent and a target. As used herein, “target”refers to a nucleic acid comprising nucleotide 1077 of SEQ ID NO: 1 or apeptide comprising amino acid 315 of SEQ ID NO: 2. This method typicallycomprises incubating a sample comprising a target with the array underconditions such that the target may associate with the epitope bindingagent attached to the array. The association may then be detected, usingmeans commonly known in the art, such as fluorescence. “Association,” asused in this context, may refer to hybridization, covalent binding, orionic binding. A skilled artisan will appreciate that conditions underwhich association may occur will vary depending on the epitope bindingagent, the substrate, the sample, and the detection method utilized. Assuch, suitable conditions may have to be optimized for each individualarray created.

In yet another embodiment, the array may be used as a tool in a methodfor determining whether a subject is at risk for developing a TDP-43proteinopathy. Similarly, the array may be used as a tool in a methodfor determining whether a subject is at risk for a MND. Alternatively,the array may be used as a tool in a method for determining whether asubject is at risk for ALS. In another alternative, the array may beused as a tool in a method for determining whether a subject is at riskfor FTLD. Typically, such a method comprises incubating the array with abiological sample from the subject. If the biological sample comprises anucleic acid comprising nucleotide 1077 of SEQ ID NO: 1, or a peptidecomprising amino acid 315 of SEQ ID NO: 2, then an association betweenthe array and the sample may be detected, and the subject may be at riskfor developing a TDP-43 proteinopathy.

In certain embodiments, the array may be used as a tool in a method fordiagnosing a subject with a TDP-43 proteinopathy. Similarly, the arraymay be used as a tool in a method for diagnosing a subject with a MND.Alternatively, the array may be used as a tool in a method fordiagnosing a subject with ALS. In another alternative, the array may beused as a tool in a method for diagnosing a subject with a FTLD.Typically, such a method comprises incubating the array with abiological sample from the subject. If the biological sample comprises anucleic acid comprising nucleotide 1077 of SEQ ID NO: 1, or a peptidecomprising amino acid 315 of SEQ ID NO: 2, then an association betweenthe array and the sample may be detected, and the subject may bediagnosed with a TDP-43 proteinopathy.

In each of the above embodiments, the subject may not display clinicalsigns of MND, ALS, or FTLD. In some embodiments, the subject may displayonly a few clinical signs of MND, ALS or FTLD.

The following examples are included to demonstrate preferred embodimentsof the invention. It should be appreciated by those of skill in the artthat the techniques disclosed in the examples that follow representtechniques discovered by the inventors to function well in the practiceof the invention. Those of skill in the art should, however, in light ofthe present disclosure, appreciate that many changes can be made in thespecific embodiments that are disclosed and still obtain a like orsimilar result without departing from the spirit and scope of theinvention, therefore all matter set forth or shown in the accompanyingdrawings is to be interpreted as illustrative and not in a limitingsense.

EXAMPLES

The following examples illustrate various iterations of the invention.

Methods

Genetic analysis. High molecular weight DNA was extracted from wholeblood, serum or brain tissue according to standard procedures. DNA fromserum was whole-genome amplified using the REPLI-g® Midi Kit (QiagenInc., Valencia, Calif., USA) prior to genetic analysis. DNA from asingle affected individual from each family was used for sequencing ofTDP-43. All exons and the intron-exon boundaries of the TDP-43 gene wereamplified using gene specific intronic primers. Direct sequencing of theamplified fragments was performed using the Big Dye Terminator CycleSequencing Ready Reaction Kit (Applied Biosystems, Wellesley, Mass.,USA) and standard protocols. For most of the fragments the primers usedfor sequencing were the same as those used for PCR amplification.Reactions were run on an ABI3130 and mutation analysis was performedusing Sequencher software v4.6 (Gene Codes Corporation, Ann Arbor,Mich., USA). Positive calls for sequence variants were made only if thevariant was observed in both forward and reverse sequence reads. Wherepossible, sequence variants were tested for segregation with the diseaseand screened in a set of 1,505 unrelated ethnically-matched controls.

Example 1

Screening

Mutation analysis of the TDP-43 gene was undertaken in 8 families withMND/ALS with an autosomal dominant pattern of inheritance and nomutation within the SOD1 gene, 5 families with familial FTLD-MND, and 25families with FTLD-U.¹⁴ All families were of European descent. Nosporadic cases of MND were available, but additional sporadic cases ofFTLD-MND (n=6) and FTLD-U (n=28) were investigated.

This analysis led to the identification of a missense mutation,Ala-315-Thr (c.1077G>A) within exon 6. In TDP-43 this alanine residue ishighly conserved throughout the evolutionary spectrum from Homo sapiensto Xenopus tropicalis, supporting its likely functional importance(Table 2). The A315T mutation segregated with all affected members of anautosomal dominant MND family (additional non-coding sequence variantswere also identified in cases with FTLD-U, FTLD-MND, and MND see FIG. 1b & c and Table 3). This mutation was absent from a large series ofethnically matched elderly controls (n=1,505).

The phenotype of the four affected family members with the TDP-43 A315Tmutation involved a slowly progressive lower motor neuron degenerationsyndrome with respiratory involvement, with only minimal involvement ofupper motor or bulbar neurons and absence of dementia (Table 3). Brainautopsy in this kindred remains to be undertaken. Similar clinicalphenotypes have been reported in sporadic MND and in kindreds with SOD1mutations.^(5,6) The TDP-43 mutation in familial MND reported heresupplements other familial neurodegenerative conditions that affectpredominantly lower motor neurons including mutations in thevesicle-associated membrane protein-associated protein B (VAPB),dynactin (DCTN1), alsin (ALS2), immunoglobulin μ binding protein 2(IGHMBP2), and glycyl-tRNA synthetase (GARS) genes, and other mutationsin juvenile MND, although some of these mutations have been identifiedin motor neuron diseases and hereditary motor neuropathies with variableclinical phenotypes.¹⁵

These data have important implications for both sporadic and familialforms of MND and FTLD-U, which are linked by a common molecularpathology: TDP-43 proteinopathy. The discovery of a missense mutation inTDP-43 in a family with dominantly inherited MND provides evidence of adirect link between TDP-43 function and neurodegeneration.

Example 2

Clinical Family Analysis

The proband (subject III-1 of FIG. 1 d)) developed weakness and atrophyof his right hand at age 48 years. Leg strength, mental status, cranialnerves, sensory examination, reflexes, coordination and gait were normalat initial examination; upper motor neuron findings were absent. Motorand sensory nerve conduction was normal, but electromyography (EMG)showed denervation in the arms both proximally and distally, withfasciculation potentials in the legs, and occasional large motor unitpotentials. Magnetic resonance imaging (MRI) of brain and spinal cordwere normal, as was blood work including absent anti-GM1 antibodies;SOD1 gene testing was normal. Three years later his upper extremityweakness had progressed but mental status, cranial nerve function, legstrength, and sensation remained normal.

The proband's father (subject II-2) developed a left foot drop at age72. Exam showed atrophy and distal weakness in the left foot,fasciculations, and increased deep tendon reflexes without otherabnormalities. EMG revealed widespread fasciculations with denervationchanges in the legs and paraspinous muscles. Weakness steadilyprogressed to involve all four extremities with respiratory andswallowing difficulty, and he died of respiratory compromise seven yearsafter diagnosis.

Subject II-3 developed left foot drop at age 64, which progressed toinvolve both legs and his arms within two years. Examination at age 69showed symmetric proximal and distal weakness in the upper extremities,with asymmetric (left>right) distal predominant weakness in the legs.Reflexes were brisk throughout. Electrophysiology showed normal sensoryand motor nerve conduction, with denervation changes in both the upperand lower extremities. Respiratory weakness developed at age 72 years,and he died of respiratory complications at age 73 years.

Subject II-4 developed right leg weakness at age 83, which progressed toinvolve both legs requiring wheelchair dependence within two years.Asymmetric arm weakness and respiratory weakness developed at age 85 andat age 86 there was severe atrophy and weakness in the lower and upperextremities with widespread fasciculations.

For more details, see Table 4.

TABLE 2TDP-43 protein (291-340 amino acids) displays high similarity betweenspecies. Residues underlined indicate differences when compared tohumans. TDP-43 A315T location is indicated in bold italic. SEQ. IDSpecies 291-340 NO. HomoNSRGGGAGLGNNQGSNM--GGGMNFGAFSINPAMMAAAQAALQSSWGMMGML  5 sapiens PanNSRGGGAGLGNNQGSNM--GGGMNFGAFSINPAMMAAAQAALQSSWGMMGML  6 troglodytesMacaca NSRGGGAGLGNNQGSNM--GGGMNFGAFSINPAMMAAAQAALQSSWGMMGML  7 mulattaBos Taurus NSRGGGAGLGNNQGSNM--GGGMNFGAFSINPAMMAAAQAALQSSWGMMGML  8Felis catus  NSRGGGAGLGNNQGSNM--GGGMNFGAFSINPAMMAAAQAALQSSWGMMGML  9Cavia N-RGGGAGLGNNQGSNM--GGGMNFGAFSINPAMMAAAQAALQSSWGMMGML 10 porcellusRattus NSRGGGAGLGNNQGGNM--GGGMNFGAFSINPAMMAAAQAALQSSWGMMGML 11norvegicus Mus NSRGGGAGLGNNQGGNM--GGGMNFGAFSINPAMMAAAQAALQSSWGMMGML 12musculus Gallus NSRGGGGGLGNNQGSNM--GGGMNFGAFSINPAMMAAAQAALQSSWGMMGML 13genus Xenopus NSRPSSGALGNNQGGNMGGGGGMNFGAFSINPAMMAAAQAALQSSWGMMGML 14tropicalis

TABLE 3 Nucleotide Amino Pathological Position Region change acidentities Frequency c.1-430 5′UTR G > A n/a MND 0.04a c.332 Ex 2 T > C A66 A MND, FTLD- 0.01087b MND, control c.848 + 69 In 5-6 ′+/G n/a MND,FTLD- 0.25c MND, FTLD-U, control c.1077 Ex 6 G > A A 315 T MND 0.0003dc.2076 3′UTR G > A n/a MND, FTLD-U 0.0072e c.3674 3′UTR +/GTTTT n/a MND,FTLD- 0.8409f MND, FTLD-U, control (numbering corresponds topolymorphism location with respect to NM_007375); Frequency based onnumber of chromosomes screened (a) 60/1,390, (b) 3/276, (c) 19/76, (d)1/3,010, (e) 2/276, (f) 37/44). With 276 chromosomes screened and apopulation frequency of 1%, the power to detect a variant is 0.94.

TABLE 4 Clinical features of a family with MND with a TDP-43 A315Tvariant. Fibs = fibrillations; PSW = positive sharp waves; SNAP =sensory nerve action potential. Electrophysiology Age at Nerve onset/Clinical findings conductions death Mental Cranial Respiratory Site ofDisease (age Subject (years) status nerves involvement onset courseperformed) Electromyography II-2 72/79 Normal Normal Yes LeftProgressive Normal Fibs/PSW lower asymmetric SNAP in legs, extremitylower motor amplitudes, thoracic neuron loss normal paraspinous in legssensory and muscles. before motor Reduced arms, distal velocitiesrecruitment. before (72) Occasional proximal. large motor Brisk units.reflexes. Fasciculations Death from throughout. respiratory weakness.II-3 64/74 Normal Normal Yes Left Progressive Normal Fibs/PSW lowerasymmetric SNAP in legs and extremity lower motor amplitudes, arms.neuron loss normal Reduced in legs sensory and recruitment. before motorOccasional arms, distal velocities large motor and (68) units. proximal.Fasciculations Brisk throughout. reflexes. Death from respiratoryweakness. II-4 83 Normal Normal Yes Right Progressive Not available Notlower asymmetric available extremity lower motor neuron loss, distal andproximal, legs before arms. Brisk reflexes. III-1 48 Normal Normal NoRight Progressive Normal Fibs/PSW upper asymmetric SNAP in arms.extremity lower motor amplitudes, Fasciculations neuron normal in loss,distal sensory and arms/legs before motor proximal, velocities arms (49)before legs.

References

-   1. Arai T, Hasegawa M, Akiyama H, et al. Biochem Biophys Res Commun    2006; 351:602-611.-   2. Neumann M, Sampathu D M, Kwong L K et al. Science 2006;    314:130-133.-   3. Cairns N J, Neumann M, Bigio E H, et al. Am J Pathol 2007;    171:227-240.-   4. Mackenzie I R A, Bigio E H, Ince P G, et al. Ann Neurol 2007;    61:427-434.-   5. Siddique T, Lalani I. Adv Neurol 2002; 88:21-32.-   6. Pasinelli P, Brown R H, Nat Rev Neurosci 2006; 7:710-723.-   7. Coate A, Chartier-Harlin M C, Mullan M, et al. Nature 1991;    349:704-706.-   8. Polymeropoulos MH, Lavedan C, Leroy E, et al. Science 1997;    276:2045-2047.-   9. Hutton M, Lendon C L, Rizzu P, et al. Nature 1998; 393:702-705.-   10. Wang H Y, Wang I F, Bose J, Shen C K. Genomics 2004; 83:130-139.-   11. Ou S H, Wu F, Harrich D, et al. J Virol 1995; 69:3584-3596.-   12. Buratti E, Dork T, Zuccato E. et al. EMBO J 2001; 20:1774-1784.-   13. Ayala Y M, Pantano S, D'Ambrogio A. et al. J Mol Biol 2005;    348:575-588.-   14. Cairns N J, Bigio E H, Mackenzie I R A, et al. Acta Neuropathol    2007; 114:5-22.-   15. Strong M J (ed). 2006. Dementia and Motor Neuron Disease.    Informa, Oxford, UK

What is claimed is:
 1. An isolated nucleic acid comprising at least tencontiguous nucleotides, including nucleotide 1077, of SEQ ID NO:
 1. 2.The isolated nucleic acid of claim 1, comprising at least twentycontiguous nucleotides, including nucleotide 1077, of SEQ ID NO:
 1. 3.The isolated nucleic acid of claim 1, consisting of SEQ ID NO:
 1. 4. Anisolated peptide comprising at least ten contiguous amino acids,including amino acid 315, of SEQ ID NO: 2
 5. The isolated peptide ofclaim 4, comprising at least twenty amino acids, including amino acid315, of SEQ ID NO: 2
 6. The isolated peptide of claim 4, consisting ofthe amino acid sequence of SEQ ID NO:
 2. 7. A method for identifying asubject at risk for a TDP-43 proteinopathy, the method comprisingdetermining the identity of the nucleotide at position 1077 of anucleotide sequence comprising the nucleic acid sequence of SEQ ID NO: 1in a sample from a subject, wherein the presence of a G instead of an Aat nucleotide 1077 indicates a risk for a TDP-43 proteinopathy.
 8. Themethod of claim 7, wherein the proteinopathy is selected from the groupcomprising MND and FTD.
 9. The method of claim 8, wherein the FTD isFTLD-U.
 10. The method of claim 8, wherein the MND is ALS.
 11. A methodfor identifying a subject at risk for a TDP-43 proteinopathy, the methodcomprising determining the identity of the amino acid at position 315 ofan amino acid sequence comprising the amino acid sequence of SEQ ID NO:2 in a sample from a subject, wherein the presence of a threonineinstead of an alanine at amino acid 315 indicates a risk for a TDP-43proteinopathy.
 12. The method of claim 11, wherein the proteinopathy isselected from the group comprising MND and FTD.
 13. The method of claim12, wherein the FTD is FTLD-U.
 14. The method of claim 12, wherein theMND is ALS.
 15. An array comprising a substrate having at least oneaddress, the address comprising an epitope binding agent that canspecifically bind to either: (a) SEQ ID NO: 1 or a portion thereofcontaining nucleotide 1077; or (b) SEQ ID NO: 2 or a portion thereofcontaining amino acid
 315. 16. The array of claim 15, wherein thesubstrate has no more than 500 addresses.
 17. The array of claim 15,wherein the substrate has more than 500 addresses.
 18. The array ofclaim 15, further comprising an address that can specifically bind toSEQ ID NO: 3 or a portion thereof containing nucleotide
 1077. 19. Thearray of claim 15, further comprising an address that can specificallybind to SEQ ID NO: 4 or a portion thereof containing amino acid
 315. 20.The array of claim 15, wherein the epitope binding agent is a nucleicacid.